diff --git a/rego/rego.go b/rego/rego.go
index a4ab65182f..0e7c63ef4d 100644
--- a/rego/rego.go
+++ b/rego/rego.go
@@ -1494,7 +1494,7 @@ func (r *Rego) compileModules(ctx context.Context, txn storage.Transaction, m me
 			Ctx:          ctx,
 			Store:        r.store,
 			Txn:          txn,
-			Compiler:     r.compiler.WithPathConflictsCheck(storage.NonEmpty(ctx, r.store, txn)),
+			Compiler:     r.compilerForTxn(ctx, r.store, txn),
 			Metrics:      m,
 			Bundles:      r.bundles,
 			ExtraModules: r.parsedModules,
@@ -1717,7 +1717,7 @@ func (r *Rego) partialResult(ctx context.Context, pCfg *PrepareConfig) (PartialR
 	}
 
 	r.metrics.Timer(metrics.RegoModuleCompile).Start()
-	r.compiler.Compile(r.compiler.Modules)
+	r.compilerForTxn(ctx, r.store, r.txn).Compile(r.compiler.Modules)
 	r.metrics.Timer(metrics.RegoModuleCompile).Stop()
 
 	if r.compiler.Failed() {
@@ -1947,6 +1947,12 @@ func (r *Rego) getTxn(ctx context.Context) (storage.Transaction, transactionClos
 	return txn, closer, nil
 }
 
+func (r *Rego) compilerForTxn(ctx context.Context, store storage.Store, txn storage.Transaction) *ast.Compiler {
+	// Update the compiler to have a valid path conflict check
+	// for the current context and transaction.
+	return r.compiler.WithPathConflictsCheck(storage.NonEmpty(ctx, store, txn))
+}
+
 func isTermVar(v ast.Var) bool {
 	return strings.HasPrefix(string(v), ast.WildcardPrefix+"term")
 }
diff --git a/rego/rego_test.go b/rego/rego_test.go
index 83ca06146e..33dc67dc8a 100644
--- a/rego/rego_test.go
+++ b/rego/rego_test.go
@@ -1035,6 +1035,38 @@ func TestPreparedPartialResultWithTracer(t *testing.T) {
 	}
 }
 
+func TestPartialResultSetsValidConflictChecker(t *testing.T) {
+	mod := `
+	package test
+	p {
+		true
+	}
+	`
+
+	c := ast.NewCompiler().WithPathConflictsCheck(func(_ []string) (bool, error) {
+		t.Fatal("Conflict check should not have been called")
+		return false, nil
+	})
+
+	r := New(
+		Query("data.test.p"),
+		Module("test.rego", mod),
+		PartialNamespace("test_ns1"),
+		Compiler(c),
+	)
+
+	ctx := context.Background()
+	pr, err := r.PartialResult(ctx)
+
+	if err != nil {
+		t.Fatalf("unexpected error from Rego.PartialResult(): %s", err.Error())
+	}
+
+	r2 := pr.Rego()
+
+	assertEval(t, r2, "[[true]]")
+}
+
 func TestMissingLocation(t *testing.T) {
 
 	// Create a query programmatically and evaluate it. The Location information
diff --git a/server/server_test.go b/server/server_test.go
index 4141e23fbf..185baa161d 100644
--- a/server/server_test.go
+++ b/server/server_test.go
@@ -3527,6 +3527,53 @@ func TestServerReloadTrigger(t *testing.T) {
 	}
 }
 
+func TestServerClearsCompilerConflictCheck(t *testing.T) {
+	f := newFixture(t)
+	store := f.server.store
+	ctx := context.Background()
+
+	// Make a new transaction
+	params := storage.WriteParams
+	params.Context = storage.NewContext()
+	txn := storage.NewTransactionOrDie(ctx, store, params)
+
+	// Fresh compiler we will swap on the manager
+	c := ast.NewCompiler()
+
+	// Add the policy we want to use
+	c.Compile(map[string]*ast.Module{"test": ast.MustParseModule("package test\np=1")})
+	if len(c.Errors) > 0 {
+		t.Fatalf("Unexpected compile errors: %v", c.Errors)
+	}
+
+	// Add in a "bad" conflict check
+	c = c.WithPathConflictsCheck(func(_ []string) (bool, error) {
+		t.Fatal("Conflict check should not have been called")
+		return false, nil
+	})
+
+	// Set the compiler on the transaction context and commit to trigger listeners
+	plugins.SetCompilerOnContext(params.Context, c)
+
+	if err := store.UpsertPolicy(ctx, txn, "test", []byte("package test\np = 1")); err != nil {
+		panic(err)
+	}
+	if err := store.Commit(ctx, txn); err != nil {
+		panic(err)
+	}
+
+	// internal helpers should now give the new compiler back
+	if f.server.getCompiler() != c {
+		t.Fatalf("Expected to get the updated compiler")
+	}
+
+	// If we request for partial evaluation it will end up using the compiler set from the manager. Ensure it
+	// is using a correct conflict checker.
+	if err := f.v1(http.MethodGet, "/data/test?partial", "", 200, `{"result": {"p": 1}}`); err != nil {
+		t.Fatalf("Unexpected error from server: %v", err)
+	}
+}
+
 type queryBindingErrStore struct {
 	storage.WritesNotSupported
 	storage.PolicyNotSupported